Contacts of the helix formed by residues 85 - 103 (chain B) in PDB entry 3H8E
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 85 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B ALA 4.0 1.0 + - - -
84B LEU* 1.3 76.7 - - - +
86B ASP* 1.3 66.1 + - - -
87B ARG 3.3 2.9 - - - -
88B THR* 3.3 11.4 + - - -
89B TRP* 2.9 21.6 + - - +
117B VAL* 4.5 0.4 - - - -
118B ASN* 4.6 9.9 - - - -
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Residues in contact with ASP 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B GLY* 1.3 70.8 - - - -
87B ARG* 1.3 60.8 + - - +
89B TRP* 3.3 4.4 + - - +
90B ARG* 2.8 36.5 + - - +
117B VAL* 3.8 4.2 - - - +
118B ASN 4.4 3.9 + - - +
120B ARG* 2.8 47.3 + - - +
129B LEU* 3.4 20.8 - - + +
408B LYS 4.8 0.5 - - - +
411B ASP* 3.9 18.8 - - - +
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Residues in contact with ARG 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A GLU* 3.2 38.1 + - + +
85B GLY 3.3 0.8 - - - -
86B ASP* 1.3 80.7 - - - +
88B THR* 1.3 59.9 + - - +
90B ARG* 3.4 17.0 + - - +
91B LYS* 2.9 63.2 + - - +
411B ASP* 2.8 42.6 + - - -
413B ARG* 3.7 8.7 - - - +
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Residues in contact with THR 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B PRO* 3.6 33.3 - - + +
84B LEU* 3.9 19.5 - - + -
85B GLY* 3.3 17.2 + - - -
87B ARG* 1.3 75.6 - - - +
89B TRP* 1.3 61.5 + - - +
91B LYS* 3.4 7.2 + - - +
92B LEU* 2.9 28.6 + - - +
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Residues in contact with TRP 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B LEU* 4.1 11.0 - - + +
85B GLY 2.9 17.5 + - - +
86B ASP 3.6 2.2 - - - +
88B THR* 1.3 77.6 - - - +
90B ARG* 1.3 64.3 + - + +
92B LEU* 3.2 25.9 + - + +
93B VAL* 3.0 30.0 + - + +
112B LEU* 4.1 12.8 - - + -
115B VAL* 3.8 30.7 - - + -
117B VAL* 3.5 32.3 - - + +
126B LYS* 2.9 52.2 + - + -
129B LEU* 3.9 22.7 - - + -
130B LEU* 3.5 39.5 - - + +
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Residues in contact with ARG 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ASP 2.8 17.8 + - - +
87B ARG* 3.8 14.7 - - - +
89B TRP* 1.3 77.6 - - + +
91B LYS* 1.3 56.6 + - + +
93B VAL* 3.3 5.9 + - - -
94B ALA* 2.9 29.0 + - - +
129B LEU* 3.7 33.6 + - + +
132B GLU* 3.6 37.2 + - - +
133B THR* 2.7 37.5 + - + +
410B ALA 4.2 5.3 + - - -
411B ASP* 3.0 49.1 + - - +
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Residues in contact with LYS 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A GLU* 5.2 8.3 + - - -
57B GLY* 5.5 0.7 - - - -
87B ARG* 2.9 49.9 + - + +
88B THR* 3.8 6.5 - - - +
90B ARG* 1.3 68.7 - - + +
92B LEU* 1.3 60.3 + - - +
94B ALA* 3.7 6.4 - - + +
95B SER* 2.8 34.0 + - - +
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Residues in contact with LEU 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B PRO* 6.5 0.2 - - + -
56B PRO* 5.1 2.0 - - + -
57B GLY* 3.1 26.9 - - - +
76B VAL* 2.8 42.4 - - + -
77B GLY 3.4 8.7 - - - +
78B SER* 5.4 2.5 - - - -
84B LEU* 5.0 8.1 - - + -
88B THR 2.9 14.7 + - - +
89B TRP* 3.4 35.2 - - + +
91B LYS* 1.3 74.1 - - - +
93B VAL* 1.3 67.8 + - - +
95B SER* 3.2 2.8 + - - -
96B VAL* 3.0 22.6 + - + +
112B LEU* 4.3 16.8 - - + -
115B VAL* 5.8 2.9 - - + -
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Residues in contact with VAL 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B TRP* 3.0 30.6 + - + +
90B ARG* 3.6 7.9 - - - +
91B LYS 3.3 0.2 - - - -
92B LEU* 1.3 80.3 - - + +
94B ALA* 1.3 57.5 + - - +
96B VAL* 3.2 7.8 + - + +
97B ALA* 2.9 26.7 + - - +
110B LEU* 5.5 4.7 - - + -
112B LEU* 5.1 2.5 - - + -
130B LEU* 3.7 59.5 - - + +
133B THR* 4.0 12.3 - - + -
134B LEU* 4.3 13.5 - - + +
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Residues in contact with ALA 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ARG 2.9 17.1 + - - +
91B LYS* 3.7 7.6 - - + +
92B LEU 3.3 0.2 - - - -
93B VAL* 1.3 76.3 - - - +
95B SER* 1.3 57.2 + - - +
97B ALA* 3.3 7.5 + - - +
98B GLY* 2.9 26.0 + - - -
133B THR* 4.0 14.3 - - + +
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Residues in contact with SER 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B GLY* 3.5 32.2 + - - -
59B THR* 5.0 3.4 - - - -
91B LYS* 2.8 18.7 + - - +
92B LEU* 3.4 9.4 - - - -
94B ALA* 1.3 72.1 - - - +
96B VAL* 1.3 66.8 + - - +
98B GLY* 3.3 3.0 + - - -
99B VAL* 3.2 26.3 + - - +
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Residues in contact with VAL 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B VAL* 3.9 24.2 - - + -
59B THR* 5.1 1.3 - - + -
74B LEU* 4.0 13.2 - - + -
76B VAL* 3.7 36.6 - - + -
92B LEU* 3.0 22.4 + - + +
93B VAL* 3.5 10.3 - - + +
95B SER* 1.3 77.9 - - - +
97B ALA* 1.4 64.5 + - - +
99B VAL* 3.1 6.3 + - - +
100B LEU* 3.0 38.3 + - + +
110B LEU* 4.1 11.9 - - + -
112B LEU* 5.2 3.8 - - + -
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Residues in contact with ALA 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B VAL 2.9 16.6 + - - +
94B ALA* 3.7 8.5 - - - +
96B VAL* 1.4 80.5 - - - +
98B GLY* 1.4 51.6 + - - +
100B LEU* 3.3 9.4 + - - +
101B LYS* 2.8 55.9 + - - +
133B THR* 5.8 1.3 - - + +
134B LEU* 4.0 29.4 - - + +
137B GLY* 6.3 1.6 - - - -
154B LEU* 6.1 0.9 - - - -
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Residues in contact with GLY 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B ALA 2.9 16.7 + - - -
95B SER* 3.3 2.7 + - - -
96B VAL 3.2 0.6 - - - -
97B ALA* 1.4 72.3 - - - +
99B VAL* 1.3 66.0 + - - +
101B LYS* 3.6 10.3 + - - +
102B GLY* 3.5 12.3 + - - -
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Residues in contact with VAL 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B THR* 4.0 29.2 - - + +
61B LEU* 4.7 8.5 - - + -
74B LEU* 4.0 24.7 - - + -
95B SER 3.2 13.2 + - - +
96B VAL 3.1 7.4 + - - +
98B GLY* 1.3 77.3 - - - +
100B LEU* 1.3 63.9 + - - +
102B GLY* 3.0 12.8 + - - -
103B LEU* 3.3 30.3 + - + +
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Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B THR* 3.8 35.2 - - + -
19B VAL* 4.4 1.8 - - + -
74B LEU* 4.3 12.3 - - + -
96B VAL* 3.0 36.2 + - + +
97B ALA* 3.9 7.2 - - - +
99B VAL* 1.3 77.4 - - - +
101B LYS* 1.3 62.4 + - - +
103B LEU* 3.1 30.2 + - + +
105B GLY 5.3 0.9 - - - +
108B ALA* 3.7 22.9 - - + -
110B LEU* 4.5 9.2 - - + -
134B LEU* 5.7 3.6 - - + -
154B LEU* 4.0 32.0 + - + +
157B VAL* 5.0 4.0 - - + -
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Residues in contact with LYS 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B ALA* 2.8 43.4 + - - +
98B GLY* 4.1 8.8 - - - +
99B VAL 3.2 0.2 - - - -
100B LEU* 1.3 74.4 - - - +
102B GLY* 1.3 59.0 + - - +
103B LEU 3.6 5.2 + - - +
134B LEU* 5.6 0.9 - - - -
137B GLY* 2.8 31.0 + - - -
138B GLU* 3.1 26.9 - - - +
152B ARG* 3.5 52.6 - - - +
153B ALA 5.3 0.7 + - - -
154B LEU* 4.7 13.9 - - + -
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Residues in contact with GLY 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B GLY 3.5 6.6 + - - -
99B VAL 3.0 9.3 + - - -
101B LYS* 1.3 76.6 - - - +
103B LEU* 1.3 65.5 + - - +
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Residues in contact with LEU 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B THR* 3.7 22.0 - - - +
61B LEU* 3.8 29.6 - - + -
72B ARG* 4.0 18.6 - - - +
99B VAL* 3.3 25.6 - - + +
100B LEU* 3.1 29.6 + - + +
101B LYS 3.9 5.0 - - - +
102B GLY* 1.3 85.1 - - - +
104B ASN* 1.3 59.7 + - - +
105B GLY* 3.3 12.0 + - - +
153B ALA* 3.8 11.4 + - - +
154B LEU 5.0 0.3 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il